[yt-users] Bug loading Ramses data

[Matthew Turk]

Hi Sam,

Running the symbol through c++filt gives that it resolves back to
std::ios_base::Init::~Init().  My guess is that this means we need an
additional "-lstdc++" in the linking line.  Can you try changing, in:

~/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/setup.py

the call to add_extension by adding:

libraries=["stdc++"],

so that it looks like this:

    config.add_extension("_ramses_reader",
        ["yt/frontends/ramses/_ramses_reader.pyx"],
        language="c++",
        include_dirs=["yt/frontends/ramses/ramses_headers/"],
        libraries=["stdc++"],
        depends=glob.glob("yt/frontends/ramses/ramses_headers/*.hh")
        )

and then forcing a rebuild with:

cd ~/Programming/yttest/yt-x86_64/src/yt-hg/
python2.7 setup.py build_ext -i -f

And seeing if that fixes it?

-Matt

On Tue, May 31, 2011 at 9:33 AM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
> Hi,
>
> I've recently installed YT and I'm getting an error in _ramses_reader.so
> when I start up YT; error message below. It's missing symbol
> _ZNSt8ios_base4InitD1Ev; Googling appears to suggest that it's related to
> Scipy. Am I missing something in the install? Let me know if you need any
> more information to unpick this one.
>
> Thanks!
>
> Sam
>
> -------
> samgeen at service0:~/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses>
> python
> Python 2.7.1 (r271:86832, May 31 2011, 13:44:37)
> [GCC Intel(R) C++ gcc 4.3 mode] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from yt.mods import *
> yt : [DEBUG    ] 2011-05-31 15:57:47,986 Set log level to 0
> WARNING : Can't import tables module...
> yt : [DEBUG    ] 2011-05-31 15:57:48,476 SIGUSR1 registered for traceback
> printing
> yt : [DEBUG    ] 2011-05-31 15:57:48,476 SIGUSR2 registered for IPython
> Insertion
> yt : [DEBUG    ] 2011-05-31 15:57:48,582 Registering: StaticOutput as <class
> 'yt.data_objects.static_output.StaticOutput'>
> yt : [DEBUG    ] 2011-05-31 15:57:48,593 Registering: EnzoStaticOutput as
> <class 'yt.frontends.enzo.data_structures.EnzoStaticOutput'>
> yt : [DEBUG    ] 2011-05-31 15:57:48,594 Registering:
> EnzoStaticOutputInMemory as <class
> 'yt.frontends.enzo.data_structures.EnzoStaticOutputInMemory'>
> yt : [DEBUG    ] 2011-05-31 15:57:48,599 Registering: OrionStaticOutput as
> <class 'yt.frontends.orion.data_structures.OrionStaticOutput'>
> yt : [DEBUG    ] 2011-05-31 15:57:48,603 Registering: FLASHStaticOutput as
> <class 'yt.frontends.flash.data_structures.FLASHStaticOutput'>
> yt : [DEBUG    ] 2011-05-31 15:57:48,605 Registering: TigerStaticOutput as
> <class 'yt.frontends.tiger.data_structures.TigerStaticOutput'>
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File
> "/panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/mods.py",
> line 68, in <module>
>   from yt.frontends.ramses.api import \
>  File
> "/panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/api.py",
> line 31, in <module>
>   from .data_structures import \
>  File
> "/panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py",
> line 37, in <module>
>   import _ramses_reader
> ImportError:
> /panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/_ramses_reader.so:
> undefined symbol: _ZNSt8ios_base4InitD1Ev
> --------
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